More details please.
After the furnace has turned the first time, let it run for 20 minutes then stop the call for heat. Go to the furnace and then have someone call for heat while you watch and listen.
You will hear the gas valve open and burners light... noise now?
In a few minutes the main blower will start... noise now?
Try and determine at what point in the start-up cycle the noise occurs. It may be oil-canning... a noise that happens as the sheet metal plenums and ducting flex due to the expansion/contraction.
Or it could be bad gas ignition ( I assume a gas furnace). If it's bad (late) ignition you will want to have it serviced very quickly or, following the maintenance manual, thoroughly clean the burner, check the burner for proper air/gas mixture, check the combustion chamber and heat exchanger for any cracks and verify the ignition system.